chr6-137004764-TAAA-T

Position:

• chr6-137004764-TAAA-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000316649.10(IL20RA):​c.725-7_725-5del variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0387 in 1,386,042 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00085 (0 hom., cov: 0)
  • Exomes 𝑓: 0.043 (0 hom.)
• Consequence: IL20RA ENST00000316649.10 splice_region, splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

Genes affected

IL20RA (HGNC:6003): (interleukin 20 receptor subunit alpha) This gene encodes a member of the type II cytokine receptor family. The encoded protein is a subunit of the receptor for interleukin 20, a cytokine that may be involved in epidermal function. The interleukin 20 receptor is a heterodimeric complex consisting of the encoded protein and interleukin 20 receptor beta. This gene and interleukin 20 receptor beta are highly expressed in skin, and are upregulated in psoriasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL20RA	NM_014432.4	c.725-7_725-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000316649.10	NP_055247.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL20RA	ENST00000316649.10	c.725-7_725-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_014432.4	ENSP00000314976	P1
IL20RA	ENST00000367748.4	c.392-7_392-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1		ENSP00000356722
IL20RA	ENST00000468393.5	c.392-7_392-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		4		ENSP00000489177
IL20RA	ENST00000541547.5	c.578-7_578-5del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		2		ENSP00000437843

Frequencies

GnomAD3 genomes AF: 0.000850 AC: 124 AN: 145936 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000877

Gnomad ASJ AF: 0.000872

Gnomad EAS AF: 0.00118

Gnomad SAS AF: 0.000215

Gnomad FIN AF: 0.00509

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000840

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0689 AC: 10443 AN: 151602 Hom.: 0 AF XY: 0.0698 AC XY: 5835 AN XY: 83602

Gnomad AFR exome AF: 0.00694

Gnomad AMR exome AF: 0.103

Gnomad ASJ exome AF: 0.0862

Gnomad EAS exome AF: 0.148

Gnomad SAS exome AF: 0.0744

Gnomad FIN exome AF: 0.0707

Gnomad NFE exome AF: 0.0579

Gnomad OTH exome AF: 0.0694

GnomAD4 exome AF: 0.0431 AC: 53469 AN: 1240060 Hom.: 0 AF XY: 0.0444 AC XY: 27385 AN XY: 617436

Gnomad4 AFR exome AF: 0.00637

Gnomad4 AMR exome AF: 0.0860

Gnomad4 ASJ exome AF: 0.0616

Gnomad4 EAS exome AF: 0.132

Gnomad4 SAS exome AF: 0.0594

Gnomad4 FIN exome AF: 0.0723

Gnomad4 NFE exome AF: 0.0372

Gnomad4 OTH exome AF: 0.0449

GnomAD4 genome AF: 0.000849 AC: 124 AN: 145982 Hom.: 0 Cov.: 0 AF XY: 0.00110 AC XY: 78 AN XY: 70854

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.000877

Gnomad4 ASJ AF: 0.000872

Gnomad4 EAS AF: 0.00118

Gnomad4 SAS AF: 0.000216

Gnomad4 FIN AF: 0.00509

Gnomad4 NFE AF: 0.000840

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs5880323; hg19: chr6-137325901;